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. Author manuscript; available in PMC: 2019 Jul 31.
Published in final edited form as: Cell Rep. 2019 Apr 23;27(4):1190–1204.e3. doi: 10.1016/j.celrep.2019.03.086

Figure 2. Changes in the absolute abundance of CF pathogens drive BAL Shannon diversity differences.

Figure 2.

A. Relationship between the Shannon diversity index and bacterial DNA recovered from the first BAL obtained from each subject (BAL-1a). Bacterial DNA recovery was measured by subtracting bacterial DNA levels in patient-paired scope pre-washes from the values in subsequent BAL-1a sample; n=17 as samples from 5 subjects (i.e. 5, 6, 8, 17, and 18) were not included because BAL samples contained lower bacterial concentrations than paired scope pre-washes. B and C. Relationship between BAL Shannon diversity and total bacterial DNA levels in all 102 BALs (B) and 22 mouth rinses (C) collected (see Fig S3 for data from throat samples). Linear regression lines with 95% confidence intervals, and Pearson correlation coefficients with p-values are shown in A-C. Relationship between the absolute abundance of (D) CF pathogens and (E) non-conventional organisms and Shannon diversity indices of BALs (n=102). Linear regression lines and Pearson correlation coefficients with respective p-values are shown. F. Absolute abundance of CF pathogens and non-conventional organisms in the 25 BALs with the lowest (left) and highest (right) Shannon diversity indices (mean values for each group are indicated in black bars). (G) and (H) show data from the 102 BALs presented in (D) and (E), but plotted in terms of relative rather than absolute abundance. The relative abundance plots obscure the finding that CF pathogen abundance drive the Shannon diversity differences. Graphs include linear regression and Pearson correlation coefficients with respective p-values. Here and below taxa abundance data obtained from sequencing is the mean of 3 technical replicates. Also see Figure S3 and S4, Table S4 for Taxa abundance data and Table S5.